Object in different scene gets renamed without any warning
No, this is how blender operates and also one of it's design flaws and known limitations. The software is not very forgiving, you either need to know what you are doing or learn by mistakes - it doesn't warn the user much, every button is basically a nuclear missile launcher (though recently a prompt to quit was added). 

What you can do as a workaround is to have a watcher running on background (effectively slowing your blender) to notify you when a name is changed:

Execute a python function whenever the user interacts with the program

You can alter that script to check anything you want (even all the scenes for changes), as it is now it prints name changes of one hadrcoded object into the system console.